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Adsorption of thymine on a defined Cu(110) surface was studied using reflection-absorption infrared spectroscopy (RAIRS), temperature programmed desorption (TPD), and scanning tunnelling microscopy (STM). In addition, density functional theory (DFT) calculations were undertaken in order to further understand the energetics of adsorption and self-assembly. The combination of RAIRS, TPD, and DFT results indicates that an upright, three-point-bonded adsorption configuration is adopted by the deprotonated thymine at room temperature. DFT calculations show that the upright configuration adopted by individual molecules arises as a direct result of strong O-Cu and N-Cu bonds between the molecule and the surface. STM data reveal that this upright thymine motif self-assembles into 1D chains, which are surprisingly oriented along the open-packed [001] direction of the metal surface and orthogonal to the alignment of the functional groups that are normally implicated in H-bonding interactions. DFT modelling of this system reveals that the molecular organisation is actually driven by dispersion interactions, which cause a slight tilt of the molecule and provide the major driving force for assembly into dimers and 1D chains. The relative orientations and distances of neighbouring molecules are amenable for p-p stacking, suggesting that this is an important contributor in the self-assembly process [ABSTRACT FROM AUTHOR]

The rotation of water in noble gas matrices has been studied. It is shown that the rotation-translation coupling model of Friedmann and Kimel predicts rotation line spacings, which are close to the experimental observations for H2O, D2O, and HDO, when gas phase rotation constants are used. The model gives intensity estimates in reasonable agreement with the observations for the local oscillator bands, which accompany the rotation spectrum. It also predicts the intensity variations in the bending region of H2O between neon, argon, and krypton matrices. [ABSTRACT FROM AUTHOR]

Infrared spectra of partially deuterated water trimers have been investigated. It is found that HDO(H2O)2 has a single, bound OD stretching fundamental, (HDO)2H2O two bound OD stretches. (HDO)3 has a single, bound OD stretch and (H2O)3 has a pair of bound OH stretches. Ab initio and discrete Fourier transform (DFT) calculations predict that the water trimer has C1 symmetry with six different, isoenergetic minima. These calculations consequently give three numerically different OD stretches for HDO(H2O)2, six for (HDO)2H2O, three for (HDO)3, and three bound OH stretches for (H2O)3. The connection between the observations and the pseudorotation of the trimer is discussed with the help of Wales' pseudorotation model. It is found that pseudorotation is sufficiently fast to average the effective symmetry of the A3 trimer to C3h and to eliminate the difference between the different ab initio minima for A2B. The only exception is (H2O)3 where the splitting between the different bound OH stretches is largest. Here a doublet is observed due to incomplete averaging. DFT calculations indicate that the D-bonded form of HDO(H2O)2 is between 50 and 60 cm-1 more stable than the H-bonded form. The energy difference is determined by differences in zero point vibration energy of intermolecular librations of the two forms. Attempts to measure the energy difference indicate that the energy difference is larger, of the order of 100 cm-1. [ABSTRACT FROM AUTHOR]

Several isotopologues of the water dimer have been studied in different matrices (Ne, Ar, Kr, and p-H2) at very low temperatures. A fine structure, which is more or less matrix independent and very similar for different intramolecular fundamentals of the same isotopologic dimer, is present on the high wavenumber side of the main component. The bound OD (OH) stretches of the donor have temperature dependent components. The fine structure and temperature dependency is interpreted as evidence for acceptor switching and rotation of the water dimer around its O–O axis in the matrices studied here. The slow nuclear spin equilibration in H2O inhibits the thermal equilibration between the acceptor switching states in H2O–DOH and H2O–DOD. The condensed environment slows down the acceptor switching rate compared to the gas phase. The antisymmetric stretch of the proton acceptor is assigned by combining information from different matrices with the rotation-acceptor switching model. [ABSTRACT FROM AUTHOR]

Far infrared spectra of seven different isotopologs of the water dimer have been measured in neon matrices at 2.8 K. The experiments are interpreted with the aid of density functional theory calculations, in particular the calculated harmonic isotopic shifts were utilized. All six intermolecular vibrational modes of the water dimer and the fully deuterated water dimer are assigned based the isotopic shifts induced. 31 of a total of 42 intermolecular fundamental modes of the seven different H, D, and 18O containing water dimers have been experimentally observed and assigned accordingly. The overall agreement between the calculations and the experiments of all isotopologs results in a complete and consistent description of these modes. [ABSTRACT FROM AUTHOR]

The anharmonic properties of a surface intermediate, methoxy, adsorbed on Cu(100) are investigated by surface infrared overtone spectroscopy and density-functional-theory electronic structure calculations. The anharmonicity is measured in the zero-coverage limit, and it is observed that the anharmonicity is increased upon adsorption as compared with the free methanol. By combining experiments with calculations we demonstrate that modifications of the anharmonicity of the methoxy species is indeed induced by adsorption onto the copper surface and not by the formation of the methoxy species. [ABSTRACT FROM AUTHOR]

The interfaces of the nanostructured dye-sensitized solid heterojunction TiO2/Ru­dye/CuI have been studied using photoelectron spectroscopy of core and valence levels, x-ray absorption spectroscopy and atomic force microscopy. A nanostructured anatase TiO2 film sensitized with RuL2(NCS)2 [cis-bis(4,4′-dicarboxy-2,2′-bipyridine)-bis(isothio-cyanato)-ruthenium (II)] was prepared in a controlled way using a novel combined in-situ and ex-situ (Ar atmosphere) method. Onto this film CuI was deposited in-situ. The formation of the dye—CuI interface and the changes brought upon the dye­TiO2 interface could be monitored in a stepwise fashion. A direct interaction between the dye NCS groups and the CuI is evident in the core level photoelectron spectra. Concerning the energy matching of the valence electronic levels, the photoelectron spectra indicate that the dye HOMO overlaps in energy with the Cu 3d—I5p hydrid states. The CuI grow in the form of particles, which at the initial stages displace the dye molecules causing dye—TiO2 bond breaking. Consequently, the very efficient charge injection channel provided by the dye—TiO2 carboxylic bonding is directly affected for a substantial part of the dye molecules. This may be of importance for the functional properties of such a heterojunction. [ABSTRACT FROM AUTHOR]

The structure and reactivity of methoxide adsorbed on Mo(110) was investigated using temperature programmed reaction, x-ray photoelectron, high resolution electron energy loss and infrared reflection absorption spectroscopies. Methanol decomposes through a methoxy surface intermediate on Mo(110), with dehydrogenation and carbon–oxygen bond scission occurring at ∼400 K. The structure of the methoxy moiety is dependent on coverage, by reference to data obtained using surface infrared spectroscopy in combination with selective isotopic labeling. We demonstrate that methoxy exhibits C3v symmetry, i.e., the C–O bond is normal to the surface, at coverages below 0.17 ML. However, the C–O axis begins to tilt towards the surface at higher coverages, so that at saturation coverage (0.25 ML), two distinct methoxy species with Cs symmetry are observed with an average tilt angle of 25°±15° from the surface normal. In addition, we conclusively show that the intense features at ∼2910 cm-1 in the infrared spectrum of adsorbed methoxide are due to overtones of the methyl deformation modes, gaining intensity by Fermi resonance with the symmetric carbon–hydrogen stretching mode, in contrast to previous assignments to the in-plane asymmetric C–H stretch which, we demonstrate, occurs at above 2935 cm-1. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The reactions of 2-propanol on Mo(110) were investigated using temperature programmed reaction, high resolution electron energy loss, and x-ray photoelectron spectroscopies. 2-Propanol forms 2-propoxide upon adsorption at 120 K on Mo(110). The 2-propoxide intermediate deoxygenates via selective γ C–H bond scission to eliminate propene as well as C–O bond hydrogenolysis to form trace amounts of propane. The C–O bond of 2-propoxide is estimated to be nearly perpendicular to the surface. Selective isotopic labeling was used to establish the coupling between the C–O stretch and modes associated with the hydrocarbon framework. The degree of coupling was strongly affected by bonding to the surface, primarily due to weakening of the C–O bond when 2-propoxide is bound to Mo(110). Selective isotopic labeling was, therefore, essential in making vibrational assignments and in identifying key reaction steps. Only a small kinetic isotope effect was observed during reaction of (CD3)(CH3)CHOH, consistent with a substantial component of C–O bond breaking in the transition state for propene elimination. Coupling of the C–O stretch to motion of the methyl group is also suggested to be important in the transition state for propene elimination. [ABSTRACT FROM AUTHOR]

The oxygen–water reaction on Pd(100) has been studied by electron energy loss spectroscopy (EELS) and low energy electron diffraction. A precursor complex for hydroxyl formation was identified in the ν(O–H) loss region of the vibrational spectrum when water was adsorbed on the Pd(100) p(2×2)O surface. The observations indicate that the precursor complex contains several water molecules. The formation of the water–oxygen precursor complex and thus the reaction is inhibited by the presence of hydrogen on the surface. The reaction is demonstrated to start at the defects of the p(2×2)O structure. Water does not adsorb on the perfect p(2×2)O structure above 140 K, at low pressures. [ABSTRACT FROM AUTHOR]

The C-H stretch and bend modes of ethoxy adsorbed on Cu(100) are investigated using Fourier transform infrared spectroscopy. Three fundamental stretch modes and four fundamental bend modes are assigned. In addition, five binary bend modes are identified; two combination and three overtone modes. It is demonstrated that by combining quantum mechanical ab initio electronic structure calculations and [sup 13]C isotopic labeling, a conclusive assignment of all observed modes is possible. The implications for the determination of surface/adsorbate geometry using vibrational spectroscopy are discussed. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The C-H stretch spectrum of methoxy adsorbed on Cu(100) has been measured using Fourier transform infrared spectroscopy. Fermi resonance coupling constants in methoxy are calculated using a normal mode model where the unperturbed modes were either experimentally determined or inferred from ab initio calculations performed for a methoxy-Mo model complex. The measured frequency shifts and intensity redistribution observed in the C-H stretch region are qualitatively reproduced by the calculations. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Fourier transform infrared absorption spectroscopy has been used to study the adsorption of methanol on the clean Ru(0001) surface at T